5-66345342-C-T

Variant names:

• chr5-66345342-C-T
• rs7727166
• ENST00000663200.1:n.372-20280C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663200.1(ENSG00000251391):​n.372-20280C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,872 control chromosomes in the GnomAD database, including 6,180 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6180 hom., cov: 31)
• Consequence: ENSG00000251391 ENST00000663200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

Genes affected

ENSG00000251391 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251391	ENST00000663200.1	n.372-20280C>T		intron_variant	Intron 3 of 4
ENSG00000251391	ENST00000665668.1	n.395-20280C>T		intron_variant	Intron 3 of 4
ENSG00000251391	ENST00000666197.1	n.382+22360C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41744 AN: 151756 Hom.: 6181 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.275 AC: 41739 AN: 151872 Hom.: 6180 Cov.: 31 AF XY: 0.279 AC XY: 20715 AN XY: 74152

African (AFR) AF: 0.166 AC: 6894 AN: 41446

American (AMR) AF: 0.288 AC: 4402 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1533 AN: 5132

South Asian (SAS) AF: 0.318 AC: 1525 AN: 4802

European-Finnish (FIN) AF: 0.369 AC: 3881 AN: 10504

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21330 AN: 67952

Other (OTH) AF: 0.267 AC: 563 AN: 2106

Alfa AF: 0.299 Hom.: 22116

Bravo AF: 0.264

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Benign	0.76
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7727166; hg19: chr5-65641170;